4.2.1 - release note tracking

cidgoh / GRDI_AMR_One_Health

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.

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4.2.1 - release note tracking #9

Closed cmrn-rhi closed 1 year ago

cmrn-rhi commented 1 year ago

Template Fixes:

Added the following fields to the Strain and Isolate Information and Merged tabs:
- ceftazidime_testing_standard
- ceftazidime_testing_standard_version
- ceftazidime_testing_standard_details
- ceftazidime_susceptible_breakpoint
- ceftazidime_intermediate_breakpoint
- ceftazidime_resistant_breakpoint
- ceftazidime-clavulanic_acid_resistance_phenotype
- ceftazidime-clavulanic_acid_measurement_sign
- ceftazidime-clavulanic_acid_measurement
Purpose_of_sequencing field now draws from the purpose_of_sequencing picklist instead of the purpose_of_sampling picklist. No impact users at this time since both lists contained the same entities.

Specification Changes:

Field	Change
`animal_source_of_food`	`FOODON:03411563` label updated from "Poultry" to "Poultry or game bird"
`food_product`	"Meat scrap" `FOODON:03309475` removed due to synonymy with "Meat trim" `FOODON:03309475` which was already present in this list.
`environmental_material`	"Bulk tank" `ENVO:03501407` removed (incorrect ID assignment) and new ID has been requested. "Animal manure" `ENVO:00003031` ID changed to `AGRO:00000079`. "Poultry litter" `ENVO:00003860` ID changed to `AGRO:00000080`
`host (food production name)`	`FOODON:03411563` label updated from "Poultry" to "Poultry or game bird". "Whether" changed to "Wether sheep" `FOODON:00004306`
`organism`	Still discussing with workgroup.
`taxonomic_identification_process`	New recommended field `GENEPIO:0100583` and associated picklist added.
`taxonomic_identification_process_details`	New free text recommended field `GENEPIO:0100584` added.

Specification Changes - Reference Guide Only:

Field	Change
`food_product`	"Chicken meat (ground or minced, extra lean)" `FOODON:03000392` ID corrected to `FOODON:03000396`.

cmrn-rhi commented 1 year ago

Confirmed with Andrew Scott that Ceftazidime and Ceftazidime + Clavulanic acid group were the fields missing.

Following added to spec under organisms:

Citrobacter freundii [NCBITaxon:546]
Salmonella enterica subsp. arizonae [NCBITaxon:59203]
Klebsiella oxytoca [NCBITaxon:571]
Klebsiella pneumoniae subsp pneumoniae [NCBITaxon:72407]
Klebsiella pneumoniae subsp ozaenae [NCBITaxon:574]
Enterobacter cloacae [NCBITaxon:550]

cmrn-rhi commented 1 year ago

Also added "Salmonella enterica" [NCBITaxon:28901] to provide a more general term people can use. Still need to discuss the addition of other general organism classes and addressing the "non-listeria monocytogenes listeria" class request.

cmrn-rhi commented 1 year ago

Updates to organisms based on AMR-GRDI Workgroup meeting (2022-11-14):

New Terms:

Acinetobacter sp. [NCBITaxon:472]
Citrobacter freundii [NCBITaxon:546]
Comamonas [NCBITaxon:283]
Comamonas aquatica [NCBITaxon:225991]
Enterobacter cancerogenus [NCBITaxon:69218]
Enterobacter cloacae [NCBITaxon:550]
Enterobacter hormaechei [NCBITaxon:158836]
Lelliottia amnigena [NCBITaxon:61646]
Pluralibacter gergoviae [NCBITaxon:61647]
Salmonella enterica subsp. arizonae [NCBITaxon:59203]
Klebsiella oxytoca [NCBITaxon:571]
Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407]
Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574]
Kosakonia [NCBITaxon:1330547]
Leclercia [NCBITaxon:83654]
Listeria [NCBITaxon:1637]
Ochrobactrum [NCBITaxon:528]
Providencia [NCBITaxon:586]
Providencia rettgeri [NCBITaxon:587]
Rahnella [NCBITaxon:34037]
Rahnella aquatilis [NCBITaxon:34038]
Raoultella [NCBITaxon:160674]
Salmonella enterica [NCBITaxon:28901]
Salmonella enterica subsp. arizonae [NCBITaxon:59203]
Vibrio [NCBITaxon:662]

Changed Terms:

Klebsiella pneumoniae [NCIT:C86457] -> [NCBITaxon:573]
Salmonella enterica subsp enterica -> Salmonella enterica subsp. enterica

Removed Terms:

Acinetobacter baumannii NIPH 60 NCBITaxon:1217647
Acinetobacter baumannii NIPH 80 NCBITaxon:1217629
Acinetobacter sp. Ag2 NCBITaxon:1646532
Citrobacter freundii GTC 09479 NCBITaxon:1288347
Citrobacter sp. KTE32 NCBITaxon:1169350
Citrobacter sp. MGH105 NCBITaxon:1686380
Comamonas aquatica DA1877 NCBITaxon:1457173
Enterobacter cloacae complex sp. 43444
Enterobacter cloacae complex sp. GN03164
Enterobacter cloacae str. Hanford NCBITaxon:1340854
Enterobacter cloacae UCI 49 NCBITaxon:1400154
Enterobacter hormaechei subsp. steigerwaltii NCBITaxon:299766
Enterobacter sp. BIDMC93 NCBITaxon:1686396
Enterobacter sp. SA187 NCBITaxon:1914861
Escherichia coli 1047 NCBITaxon:1411693
Escherichia coli 1365 NCBITaxon:1411697
Escherichia coli 2-011-08_S4_C1 NCBITaxon:1444201
Escherichia coli 2-156-04_S3_C2 NCBITaxon:1444150
Escherichia coli 2-210-07_S3_C1 NCBITaxon:1444122
Escherichia coli 2-316-03_S3_C1 NCBITaxon:1444124
Escherichia coli 3-105-05_S4_C3 NCBITaxon:1444278
Escherichia coli 3-267-03_S1_C2 NCBITaxon:1444085
Escherichia coli 3006 NCBITaxon:1005565
Escherichia coli 38.16 NCBITaxon:1411698
Escherichia coli 5-172-05_S4_C3 NCBITaxon:1444269
Escherichia coli 541-1 NCBITaxon:752786
Escherichia coli 6-537-08_S4_C2 NCBITaxon:1444257
Escherichia coli 7-233-03_S4_C1 NCBITaxon:1444213
Escherichia coli APEC O78 NCBITaxon:1274814
Escherichia coli C353_09 NCBITaxon:1126898
Escherichia coli chi7122 NCBITaxon:475609
Escherichia coli E1140 NCBITaxon:1453472
Escherichia coli FBP1 NCBITaxon:1412837
Escherichia coli FCP1 NCBITaxon:1412839
Escherichia coli HVH 150 (4-3258106) NCBITaxon:1281083
Escherichia coli HVH 22 (4-2258986) NCBITaxon:1280973
Escherichia coli HVH 79 (4-2512823) NCBITaxon:1281017
Escherichia coli HVH 83 (4-2051087) NCBITaxon:1281020
Escherichia coli IAI1 NCBITaxon:585034
Escherichia coli IMT8073 NCBITaxon:1337997
Escherichia coli KOEGE 3 (4a) NCBITaxon:1281153
Escherichia coli KOEGE 40 (102a) NCBITaxon:1281159
Escherichia coli KTE100 NCBITaxon:1182699
Escherichia coli KTE13 NCBITaxon:1169318
Escherichia coli KTE146 NCBITaxon:1182725
Escherichia coli KTE184 NCBITaxon:1181730
Escherichia coli KTE196 NCBITaxon:1181742
Escherichia coli KTE222 NCBITaxon:1181768
Escherichia coli KTE47 NCBITaxon:1182654
Escherichia coli MS499 NCBITaxon:1450517
Escherichia coli N1 NCBITaxon:1005567
Escherichia coli O103:H11 str. 04-3023 NCBITaxon:1446501
Escherichia coli O5:K4(L):H4 str. ATCC 23502 NCBITaxon:1268238
Escherichia coli O69:H11 str. 07-3763 NCBITaxon:1446751
Escherichia coli UMEA 3336-1 NCBITaxon:1281243
Escherichia coli UMEA 3671-1 NCBITaxon:1281260
Escherichia coli UMEA 3805-1 NCBITaxon:1281270
Escherichia fergusonii ATCC 35469 NCBITaxon:585054
Klebsiella oxytoca MGH 28 NCBITaxon:1328429
Pseudomonas sp. HMSC064G05 NCBITaxon:1715204
Pseudomonas sp. HMSC067F09 NCBITaxon:1739343
Rahnella sp. Y9602 NCBITaxon:1873497
Serratia sp. 14-2641 NCBITaxon:1841657

cmrn-rhi commented 1 year ago

Other field changes:

environmental_site

Research farm [ENVO:03501417]; new ID
Manure digester facility [ENVO:03501422]; new ID and definition
Manure lagoon (Anaerobic lagoon) [ENVO:03501423]; new ID and definition

weather_type

Cloudy/Overcast [ENVO:03501418]; new ID and definition
Partially cloudy [ENVO:03501419]; new ID and definition
Drizzle [ENVO:03501420]; new ID and definition

environmental_material

Fluid from meat rinse[GENEPIO:0004323]; new ID
Freezer [ENVO:03501415]; new ID and definition
Freezer handle [ENVO:03501414]; new ID and definition
Manure digester equipment [ENVO:03501424]; new ID and definition

anatomical_part

Swine carcass [FOODON:03311719]; new definition

food_product

Brassica carinata meal [FOODON:00004310]; new ID and definition
Sausage (whole) [FOODON:03315904]; new label and definition
Corn cob (whole or parts) [FOODON:03310791]; new label and definition
Greens (raw) [FOODON:03310765]; new definition

food_product_properties

Italian-style food product [FOODON:00004321]; new label, ID, and definition

collection_device

Culture plate [GENEPIO:0004318]; new ID and definition
Vacuum device [GENEPIO:0002127]; new definition

collection_method

Fecal grab [GENEPIO:0004326]; new ID

host (common name)

Companion animal [FOODON:03000300]; new ID

host (food production name)

Fish egg [FOODON_00004319]; new ID and definition
Fry (fish) [FOODON_00004318]; new ID and definition
Juvenile fish [FOODON_00004317]; new ID and definition

sequencing_platform

BGI Genomics [GENEPIO:0004324]; new ID
MGI [GENEPIO:0004325]; new ID

cmrn-rhi commented 1 year ago

Released v4.2.1